Population Structure and Historical Demography of the Oriental River Prawn (Macrobrachium nipponense) in Taiwan.

Chen PC, Shih CH, Chu TJ, Wang D, Lee YC, Tzeng TD - PLoS ONE (2015)

Bottom Line:
All FST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan).The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively.And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.

Affiliation: Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106, Taiwan.

ABSTRACTThe oriental river prawn (Macrobrachium nipponense) is a non-obligatory amphidromous prawn, and it has a wide distribution covering almost the entire Taiwan. Mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA were combined and used to elucidate the population structure and historical demography of oriental river prawn in Taiwan. A total of 202 individuals from six reservoirs and three estuaries were separately collected. Nucleotide diversity (π) of all populations was 0.01217, with values ranging from 0.00188 (Shihmen Reservoir, SMR, northern Taiwan) to 0.01425 (Mingte Reservoir, MTR, west-central Taiwan). All 76 haplotypes were divided into 2 lineages: lineage A included individuals from all sampling areas except SMR, and lineage B included specimens from all sampling locations except Chengching Lake Reservoir (CLR) and Liyu Lake Reservoir (LLR). All FST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan). UPGMA tree of nine populations showed two main groups: the first group included the SMR and Tamsui River Estuary (TSE) (both located northern Taiwan), and the second one included the other seven populations (west-central, southern and eastern Taiwan). Demographic analyses implied a population expansion occurred during the recent history of the species. The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively. And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.

Mentions:
The best-fitting model explaining our data was T92 model. This model was used for NJ and ML reconstruction and AMOVA analyses. Two individuals of Macrobrachium asperulum were also analyzed in NJ and ML reconstruction as outgroups. Phylogenetic tree of all haplotypes is shown in Fig 2. Bootstrap values of main node are 77 and 83 for neighbor join and Maximum Likelihood trees, respectively. All haplotypes were divided into two distinct lineages (A and B). The network for all specimens (Fig 3) supported the result obtained from the phylogenetic tree. Two sub-lineages might be found in lineage A in the network. The first sub-lineage only included individuals from YLR population, and the second one comprised the specimens from KPE and JGE populations. These two sub-lineages were also found at the basal node of the lineage A of phylogenetic tree. The distribution of lineage A and B specimens for different populations are also shown in Fig 1 and Table 1. Both individuals from lineage A and B could be found in all sampling sites except SMR, CLR and LLR. Both CLR and LLR populations only included individuals from lineage A, but SMR comprised ones from lineage B. Haplotype diversities (h) of lineage A and lineage B were 0.966 and 0.733, respectively. Nucleotide diversities (π) of lineage A was 0.00834, and the lineage B was 0.00450 (Table 1). The τ values of lineage A and lineage B were 5.215/2u and 0.932/2u generations, respectively. The average divergence rate of 1.42% / myr and a generation time of 1 year were used to calculate the time of expansion. The estimated time of expansion for lineage A was 257,902 years ago. For lineage B, the estimate was 41,435 years ago.

Mentions:
The best-fitting model explaining our data was T92 model. This model was used for NJ and ML reconstruction and AMOVA analyses. Two individuals of Macrobrachium asperulum were also analyzed in NJ and ML reconstruction as outgroups. Phylogenetic tree of all haplotypes is shown in Fig 2. Bootstrap values of main node are 77 and 83 for neighbor join and Maximum Likelihood trees, respectively. All haplotypes were divided into two distinct lineages (A and B). The network for all specimens (Fig 3) supported the result obtained from the phylogenetic tree. Two sub-lineages might be found in lineage A in the network. The first sub-lineage only included individuals from YLR population, and the second one comprised the specimens from KPE and JGE populations. These two sub-lineages were also found at the basal node of the lineage A of phylogenetic tree. The distribution of lineage A and B specimens for different populations are also shown in Fig 1 and Table 1. Both individuals from lineage A and B could be found in all sampling sites except SMR, CLR and LLR. Both CLR and LLR populations only included individuals from lineage A, but SMR comprised ones from lineage B. Haplotype diversities (h) of lineage A and lineage B were 0.966 and 0.733, respectively. Nucleotide diversities (π) of lineage A was 0.00834, and the lineage B was 0.00450 (Table 1). The τ values of lineage A and lineage B were 5.215/2u and 0.932/2u generations, respectively. The average divergence rate of 1.42% / myr and a generation time of 1 year were used to calculate the time of expansion. The estimated time of expansion for lineage A was 257,902 years ago. For lineage B, the estimate was 41,435 years ago.

Bottom Line:
All FST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan).The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively.And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.

Affiliation:
Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106, Taiwan.

ABSTRACTThe oriental river prawn (Macrobrachium nipponense) is a non-obligatory amphidromous prawn, and it has a wide distribution covering almost the entire Taiwan. Mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA were combined and used to elucidate the population structure and historical demography of oriental river prawn in Taiwan. A total of 202 individuals from six reservoirs and three estuaries were separately collected. Nucleotide diversity (π) of all populations was 0.01217, with values ranging from 0.00188 (Shihmen Reservoir, SMR, northern Taiwan) to 0.01425 (Mingte Reservoir, MTR, west-central Taiwan). All 76 haplotypes were divided into 2 lineages: lineage A included individuals from all sampling areas except SMR, and lineage B included specimens from all sampling locations except Chengching Lake Reservoir (CLR) and Liyu Lake Reservoir (LLR). All FST values among nine populations were significantly different except the one between Jhonggang River Estuary (JGE, west-central Taiwan) and Kaoping River Estuary (KPE, southern Taiwan). UPGMA tree of nine populations showed two main groups: the first group included the SMR and Tamsui River Estuary (TSE) (both located northern Taiwan), and the second one included the other seven populations (west-central, southern and eastern Taiwan). Demographic analyses implied a population expansion occurred during the recent history of the species. The dispersal route of this species might be from China to west-central and west-southern Taiwan, and then the part individuals belonging to lineage A and B dispersed southerly and northerly, respectively. And then part individuals in west-central Taiwan fell back to and stay at estuaries as the sea level rose about 18,000 years ago.